                       Changes in version 2.27.3                        

    o   Implemented XenoMix for estimating mouse content from EPIC array data in PDX models

                       Changes in version 2.27.1                        

    o   Fixed issue with nv probes. Now they are filtered during the preprocessing.

                       Changes in version 2.19.0                        

    o   Fixed issue with logical having a length greater than 1

                       Changes in version 2.17.1                        

    o   Temporarily removed the GLAD dependency and CNV functionality

                       Changes in version 2.17.0                        

    o   Fixed bug in differential variability analysis

                       Changes in version 2.15.1                        

    o   Added custom reimplementations of dye-bias and background correction methods from SeSaMe

                       Changes in version 2.13.2                        

    o   Removed support for RefFreeEWAS, since the package is not supported anymore

                       Changes in version 2.13.0                        

    o   Compatibility fixes with SeSaMe by zwdzwd

    o   Minor bugfixes

                       Changes in version 2.11.0                        

    o   Bugfixes in MMBC support

                        Changes in version 2.9.4                        

    o   Added initial version of the Mouse Methylation Bead Chip support

    o   Native implementations of basic dye-bias and background correction methods (methylumi dependency removed)

                        Changes in version 2.9.3                        

    o   Changed some of the default options values

    o   Some bugfixes

                        Changes in version 2.9.2                        

    o   Implemented function rnb.execute.pOOBAH. Thanks to Nathan Steenbuck.

    o   Update of contact information in DESCRIPTION

                        Changes in version 2.9.1                        

    o   Improved function intensities.by.color. Thanks to Nathan Steenbuck.

                        Changes in version 2.7.1                        

    o   Added conversion from RnBeadRawSet to RGChannelSet

                        Changes in version 2.3.3                        

    o   Fixed non ASCII column names in age prediction and immune estimation

                        Changes in version 2.3.2                        

    o   Added stratification plots for inferred covariates in different sample groups

                        Changes in version 2.1.3                        

    o   Implemented methylation based segmentation by the MethylSeekR approach. Thanks to Abdulrahman Salhab for providing code for the integration.

    o   Wrapper for load.rnb.set

                        Changes in version 2.1.2                        

    o   Fix in as.RnBeadRawSet

    o   Added new paper to CITATION

                        Changes in version 2.1.1                        

    o   Added support for SLURM compute cluster architecture

                       Changes in version 1.99.0                        

    o   RnBeadsDJ: updated documentation and tooltips

    o   deactivated intersample plots (exploratory module) as default option for BS-seq data

    o   Roxygen documentation updates

    o   Extended methods descriptions in reports (imputation, filtering, differential, ...)

    o   Miscellaneous bugfixes and performance improvements in RnBeadsDJ, imputation, ...

                       Changes in version 1.13.3                        

    o   added CNV estimation using the GLAD package to QC module

    o   some bugfixes

    o   changed 'gender' to 'sex', affected functions and options are 'rnb.execute.gender.prediction' and 'import.gender.prediction'

                       Changes in version 1.13.2                        

    o   added qvalue to suggested packages

                       Changes in version 1.13.1                        

    o   Updated LOLA DB download links

                       Changes in version 1.11.9                        

    o   Bugfixes and improvements in gender prediction, GEO import, differential variability, installation and others

                       Changes in version 1.11.8                        

    o   Fixes for bioconductor warnings (combine, etc.)

    o   docoupled missing value imputation from differential methylation

                       Changes in version 1.11.7                        

    o   enhanced cross-platform combination methods

    o   improved installation routines

    o   enhanced plots in exploratory analysis module

    o   better LOLA annotation

    o   improved performance of missing value imputation

    o   documentation updates

    o   several minor bugfixes

                       Changes in version 1.11.6                        

    o   Improved combining methods for RnBSet objects of different data types

    o   Interpretation of sample mean methylation levels and other statistics

    o   Improved plots in exploratory analysis module

    o   Improved missing value imputation

    o   Several minor bugfixes

                       Changes in version 1.11.5                        

    o   bugfixes (loading, imputation)

                       Changes in version 1.11.4                        

    o   Introducing RnBeadsDJ, a shiny-based interface for running RnBeads analyses and modules (run with rnb.run.dj())

    o   Added implementation of the LUMP algorithm for immune cell content estimation

    o   The default normalization method was changed to "wm.dasen"

    o   Background normalization is now disabled per default.

    o   Option backwards compatibility

    o   bugfixes (LOLA dependencies, 1-sample differential variability, QC visualization, ...)

                       Changes in version 1.11.2                        

    o   Fixed a bug concerning failed trackhub exports on Windows

                        Changes in version 1.9.4                        

    o   You can now retrieve custom region sets from the RnBeads resource using the rnb.load.annotation.from.db function

    o   improved import from GEO

    o   bigff disk dump is now the default option for dealing with disk-based big matrices

    o   Several bugfixes and performance improvements in Greedycut, normalization, Bisulfite data loading and others

    o   Added differential variability analysis in addition to differential methylation

                        Changes in version 1.9.3                        

    o   LOLA support for differentially methylated regions

    o   various LOLA utitility functions

    o   What used to be the "differential.enrichment" option is now called "differential.enrichment.go" to reflect the distinction between GO and LOLA enrichment analyses

    o   Missing methylation data can now be imputed (using mean, random or nearest-neighbor imputation)

    o   Gender prediction now supports sequencing and EPIC data

    o   Added a function for combining two array-based datasets from (potentially) different platforms.

    o   Several bugfixes and performance improvements

                        Changes in version 1.7.5                        

    o   Several minor bugfixes and performance improvements

    o   added a vignette section on working with RnBSet objects 

                        Changes in version 1.7.4                        

    o   Several minor bugfixes and performance improvements

    o   Vignette installation instructions updated

    o   Reduce warnings in R CMD check

                        Changes in version 1.7.3                        

    o   Age predictor (MethylAger) updates and documentation

    o   Support for external tools bedToBigBed and bedGraphToBigWig

    o   Minor bugfixes

                        Changes in version 1.7.2                        

    o   Added genetic purity estimation based on SNP probes (option qc.snp.purity, microarrays only)

                        Changes in version 1.7.1                        

    o   Added support for the ENmix.oob background subtraction method

    o   Several improvements in age prediction module

    o   Added conversion from minfi raw dataset to RnBeadRawSet

    o   Several minor bug fixes

                        Changes in version 1.5.1                        

    o   Reference-based cell type composition estimation now uses the 50,000 most variable sites by default.

    o   Minor bug fixes

                        Changes in version 1.3.8                        

    o   Added age prediction from 450K and bisulfite data to inference module

                        Changes in version 1.3.7                        

    o   Subsampling for reporting and plotting methylation values distributions in filtering
	  report to reduce memory footprint.

                        Changes in version 1.3.6                        

    o   Support for Illumina EPIC array and related bugfixes

    o   Added a section on whitelist and blacklist in the Preprocessing module

                        Changes in version 1.3.5                        

    o   Fixes with ggplot in 450K array QC plotting

    o   Added an option 'differential.report.sites' to decrease runtime by skipping the differential site methylation section in the report

                        Changes in version 1.3.4                        

    o   Added support for Illumina EPIC array

                        Changes in version 1.3.3                        

    o   Added 'smooth.profile' parameter to rnb.plot.locus.profile function

                        Changes in version 1.3.2                        

    o   Performance and memory improvements during loading, qc and preprocessing of large bisulfite-derived RnBSets

    o   Added optional arguments to meth() and covg() allowing for partial retrieval of methylation and coverage information from RnBSets. Particularly makes sense for large, disk-based datasets.

    o   Added option "disk.dump.bigff.finalizer" for setting the finalizer for temporary BigFfMat objects

                        Changes in version 1.3.1                        

    o   Added "remove.regions" function for RnBSet class

    o   summarize.regions now summarizes for each sample individually in order to reduce memory consumption for large WGBS datasets

    o   import.skip.object.check option for keeping the memory profile low while loading huge datasets

    o   NA sites (filtering.missing.value.quantile) are now removed even if they were previously masked (filtering.low.coverage.masking)

    o   Added "nsites" method for quickly extracting the number of sites for large RnBSet objects without having to retrieve the full methylation matrix

    o   Added "hasCovg" method for quickly determining whether coverage information is present in large RnBSet objects without having to retrieve the full coverage matrix

                        Changes in version 1.1.9                        

    o   Filtering report fix when no normalization is conducted

    o   Bugfixes for combine(RnBSet, RnBSet) and BigFf matrices

                        Changes in version 1.1.8                        

    o   Corrected coverage statistics in sample summary table: Sites with NA methylation values are no longer considered in the coverage statistics (makes a difference if some coverage threshold is applied)

    o   Improved method for gender prediction. Predicted genders are also included in the exported annotation table

                        Changes in version 1.1.7                        

    o   Improvements to mergeSamples function for RnBiseqSets

    o   Some more memory clean-up

                        Changes in version 1.1.6                        

    o   Differential methylation based on region level only is now supported

    o   Minor updates to the differential methylation report generation

    o   Performance improvements and minor bugfixes for using disk.dump.bigff

    o   Performance improvements (more memory clean-up)

                        Changes in version 1.1.5                        

    o   New option: disk.dump.bigff for using a wrapper class of the ff package to avoid their INT_MAX issue

                        Changes in version 1.1.4                        

    o   Fixes in parallel environment setup from bioconcuctor

                        Changes in version 1.1.3                        

    o   Some fixes in data loading

    o   Fixes in parallel environment setup

                        Changes in version 1.1.2                        

    o   New annotation package format

    o   Support for filtering out cross-reactive probes in Infinium 450k dataset

    o   Improved logging on a Mac

                        Changes in version 1.0.0                        

    o   Bioconductor release

                       Changes in version 0.99.23                       

    o   Incorporated some bioconductor check related improvements

                       Changes in version 0.99.22                       

    o   Incorporated bioconductor requirements for parallel processing. "parallel.disable" is now "parallel.teardown"

                       Changes in version 0.99.20                       

    o   RnBeads no longer suggests IlluminaHumanMethylation450k.db.

                       Changes in version 0.99.19                       

    o   Fixed a bug in the computation of surrogate variables (SVA) that did not take into account other adjustment variables in the model (compared to the null model)

    o   Updated locus profiles to work with the latest version of Gviz

    o   Differential methylation reports now contain information on group sizes

    o   Included plots of number of sites vs coverage percentiles for each sample in the dataset (rnb.plot.num.sites.covg)

    o   Bisulfite-seq QC reports now contain an additional section with summary statistics and plots when the coverage histogram plots are enabled

                       Changes in version 0.99.18                       

    o   Implementation of class constructors (the S4 constructors are not available anymore)

    o   Analyses can now be started from an RnBSet which is stored on the hard drive (using save.rnb.set) via the rnb.set.dir data type

    o   New IDAT loading routine, based on the illuminaio package

    o   Multiple fixes in wrappers for wateRmelon normalization methods

    o   Fixed the RefFreeEWAS wrapper

    o   Updated the Houseman, 2012 reference-based method implementation

    o   RnBSets now know the version with which they were created

    o   Various other bugfixes and improvements to reports and documentation

                       Changes in version 0.99.17                       

    o   Consistency issues with Bioconductor 3.0 fixed

    o   Fixed a bug relating to no coverage masking being conducted for sequencing data

    o   Various other bugfixes

                       Changes in version 0.99.16                       

    o   Enhanced XML-based analysis though the tag preanalysis.script

    o   Optimized loading of the sequencing data sets

    o   Enhanced region profiles plots. Added region site distribution plots

    o   Locus profiles can now be generated in the exploratory report for regions specified in custom bed files and for genes listed as gene symbols

    o   Improved cell type heterogeneity inference (no cell types excluded anymore)

    o   Added more support for paired differential methylation with limma

    o   Some functions were renamed: merge.samples->mergeSamples, add.pheno->addPheno, add.region.subsegments->addRegionSubsegments, and all functions operating on Report

    o   Added helper classes for submitting RnBeads to a scientific compute cluster. Current implementation includes Sun Grid Engine

    o   The default pipeline now uses ff functionality and saves intermediate objects into the report directory

    o   Minor bugfixes

                       Changes in version 0.99.15                       

    o   Restructuring of the pipeline modules:
	** the loading module has been renamed to import
	** the prefiltering,normalization and postfiltering modules have been summarized in a new module: preprocessing
	** the batch and profiles modules have been summarized in a new module for exploratory analysis
	** the export module has been renamed to tracks and tables
	** corresponding option names have been changed
	** see the overview figure on the website or the vignette for a quick overview on the new module structure

    o   Multiple RnBSets can now be concatenated with the add() function

    o   Multiple samples in an RnBSet can be merged using the merge.samples() function

    o   Gender prediction can be performed on Infinium 450k datasets

    o   Minor updates on covariate adjustment

    o   Updates on tissue heterogeneity estimation

    o   Calling differentially methylated sites with RefFreeEWAS now supports paired design

    o   Multiple minor bugfixes and performance improvements

    o   Vignette and documentation updates

                       Changes in version 0.99.13                       

    o   Added new module on annotation inference

    o   Added correction for cell type heterogeneity

    o   Added SVA functionality

    o   Minor bugfixes

    o   Updates to the vignette and other documentation

                       Changes in version 0.99.12                       

    o   Support Bismark coverage file loading

    o   Enhanced documentation and logging of loading steps

    o   Minor bugfixes

    o   Updates to the vignette and other documentation
	RnBeads 0.99.11

    o   Accommodate data packages for individual genomes

    o   Performance: disk space usage when using disk dumping, options for subsetting sites when computing distance matrices for clustering, PCA and MDS

    o   Region subsegmentation

    o   The default method for differential methylation p-values is limma

                       Changes in version 0.99.10                       

    o   Performance improvements

    o   Option to keep big matrices on the hard drive rather than main memory

    o   Restructuring of the filtering modules. Parts of the filtering steps are executed before normalization others afterwards

    o   Improvements in normalization: more methods supported

    o   Cosmetic changes to some of the plots

                       Changes in version 0.99.9                        

    o   Bugfixes in paired analysis

    o   Usability of bisulfite sequencing

                       Changes in version 0.99.8                        

    o   New normalization methods integrated

    o   Improved arguments to rnb.run.analysis

    o   Improved parsing of the sample annotation table

    o   Paired analysis (testing stage)

    o   Webservice installed

    o   Multiple bugfixes

                       Changes in version 0.99.7                        

    o   Support for background subtraction and BMIQ normalization of Infinium 450k data

    o   Support for differential methylation analysis on all pairs of sample groups

                       Changes in version 0.99.6                        

    o   Locus Profiles

    o   Support for parallel computing

                       Changes in version 0.99.0                        

    o   Many additional features including bisulfite sequencing mode, the mouse genome, data export, ...

                        Changes in version 0.5.0                        

    o   Initial release of RnBeads containing six modules - loading and normalization, quality control, filtering, batch effects, methylation profiles and differential methylation.
